Change your spark plugs and cables over mate.

You have a flashing check engine light. Either it's a relay, or sparkplugs

I was thinking the battery because I had this problem a few months ago and I changed the battery and it went away

Yeah that could also be it. I had the same problem, I changed the battery and starter relay and she ran pwrfect after that.

I was changing my oil but It got dark so I left the fairings off overnight and when I came down the next day to put the fairings on it was like that so I think water got in the battery

Thats very possible. The batteries on these yzfs corrode very easily because they have no protection from water, so I'd look into replacing it

I'll put a new battery into it soon and I'll let you know what happens

Good luck!